Very little is known about the developmental regulation of drug-metabolizing enzymes and transporters (together called drug-processing genes [DPGs]) in liver, placing newborns and children at a much higher risk of adverse drug reactions (ADRs). Using RNA-Seq, we have shown that drug metabolism is the top most differentially regulated pathway in the entire liver transcriptome of germ-free (GF) mice, suggesting that there is a novel interaction between gut microbiome and hepatic DPGs. One of the key functions of gut microbiome is to produce secondary bile acids (BAs), which can activate two most critical xenobiotic-sensing nuclear receptors in liver, namely the pregnane X receptor (PXR) and constitutive androstane receptor (CAR). During development, profound changes occur in the intestinal bacteria and the secondary BA profiles, suggesting that gut microbiome may at least in part contribute to the developmental regulation of DPGs in liver. No systematic studies have been performed to characterize the regulation of all DPGs by gut microbiome during development, and little is known regarding how targeting the gut microbiome by antibiotics or probiotics re- programs the ontogeny of DPGs in liver. Therefore the goal of this research is to utilize multidisciplinary approaches, including GF and genetically-engineered mice, BA metabolomics, Next-Generation Sequencing, and human fecal samples, to unveil the role of gut microbiota in modulating PXR and CAR signaling and the subsequent ontogenic re-programming of DPGs in liver. Our central hypothesis is: the developmental changes in the gut microbiome at least in part contribute to the regulation of the ontogeny of DPGs in liver, through altering secondary BAs in the gut to modify the PXR and/or CAR signaling in liver. We will test our hypothesis in 2 Aims: Aim 1A will use RNA-Seq to quantify mRNAs of 281 critical DPGs in livers of GF and conventional (Conv) mice at 6 developmental ages, and validate the proteins and activities of differentially regulated DPGs. We will also use ChIP-Seq to quantify how gut bacteria modulate PXR/CAR DNA binding to certain DPGs, and correlate DPG ontogeny with the ontogeny of gut microbiome (metagenomics) and BA profiles (UPLC-MS/MS). Aim 1B will introduce secondary BAs to GF mice in various PXR- and CAR-knockout and humanized transgenic) at various ages to test our hypothesis that secondary BAs restore the normal ontogeny of certain DPGs. Aim 2 will use GF mice colonized with human fecal bacteria from various developmental ages, to determine the roles of antibiotics and the probiotic L. acidophilus in re-programming the ontogeny of human microbiome and the subsequent changes in the host DPGs during liver development. The proposed work will unveil a novel link between the ontogeny of gut microbiome and the developmental changes of drug- processing capacities during development, and will lead to a paradigm shift in pediatric pharmacology, by establishing a new concept in considering ADRs in children, which are the bug-drug interactions, in addition to the known drug-drug and food-drug interactions.